Rationale and background:

Overview of rnaQUAST

rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene data database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party softwares (STAR, TopHat, GMAP etc.,). The detailed manual is available here - http://spades.bioinf.spbau.ru/rnaquast/release1.1.0/manual.html

Needs to run rnaQUAST on Atmosphere

Atmosphere requirements

CyVerse username that has an institutional email (e.g. janedoe@email.arizona.edu)

Part 1: Connect to an instance of an Atmosphere Image (Virtual Machine)

Step 2. Click on the Launch New Instance button and search for rnaQUAST 1.1.0.

Step 3. Select the image rnaQUAST 1.1.0 and click Launch Instance. It will take 10-15 minutes for the cloud instance to be launched.

Note: Instances can be configured for different amounts of CPU, memory, and storage depending on user needs. This tutorial can be accomplished with the medium instance size, medium1 (4 CPUs, 8 GB memory, 80 GB root)

Part 2: Set up a rnaQUAST 1.1.0 run on a test data using the Terminal window

Step 1. Open the Terminal. Add the ssh details along with your IP address to connect the instance through the terminal

step 2. You will find rnaQUAST v1.1.0 software in "/opt" folder. All the dependencies for running rnaQUAST v1.1.0 are located in "/opt/rnaQUAST-1.1.0"

Step 3. Before you start using the rnaQUAST 1.1.0, you need to make sure that the following softwares are added to your PATH

Step 4. The staged example data can be found in folder "rnaQUAST-1.1.0/test_data" within "opt" folder. List its contents with the ls command: